diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/fasta/FastaAlternateReferenceIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/fasta/FastaAlternateReferenceIntegrationTest.java
index 6d1c4b0e3..765deb0e5 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/fasta/FastaAlternateReferenceIntegrationTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/fasta/FastaAlternateReferenceIntegrationTest.java
@@ -59,23 +59,68 @@ import java.util.Arrays;
 
 public class FastaAlternateReferenceIntegrationTest extends WalkerTest {
 
+    private static String CONTIGUOUS_INTERVAL_SAME_CONTIG_MD5 = "e1f4b93f9071d158d94dc4fb25e07702";
+    private static String CONTIGUOUS_INTERVAL_DIFF_CONTIG_MD5 = "dfca4e0b0fe0cb18596ec51af541a69e";
+
     @Test
     public void testReferenceOnly() {
 
         WalkerTestSpec spec = new WalkerTestSpec(
                 "-T FastaReferenceMaker -R " + b36KGReference + " -L 1:10,000,100-10,000,500 -L 1:10,100,000-10,101,000 -L 1:10,900,000-10,900,001 -o %s",
                  1,
-                 Arrays.asList("328d2d52cedfdc52da7d1abff487633d"));
+                 Arrays.asList("75d4d352a9ce4fae22fd7924a42c800a"));
         executeTest("test FastaReference", spec);
     }
 
+    @Test
+    public void testReferenceOnlyContiguousSameContig() {
+
+        WalkerTestSpec spec = new WalkerTestSpec(
+                "-T FastaReferenceMaker -R " + b36KGReference + " -L 1:10,000,100-10,000,200 -L 1:10,000,201-10,000,301 -o %s",
+                1,
+                Arrays.asList(CONTIGUOUS_INTERVAL_SAME_CONTIG_MD5));
+        executeTest("test FastaReference with contiguous intervals, same contig", spec);
+    }
+
+    @Test
+    public void testReferenceOnlyContiguousDiffContigs() {
+
+        WalkerTestSpec spec = new WalkerTestSpec(
+                "-T FastaReferenceMaker -R " + b36KGReference + " -L 1:10,000,100-10,000,200 -L 2:10,000,201-10,000,301 -o %s",
+                1,
+                Arrays.asList(CONTIGUOUS_INTERVAL_DIFF_CONTIG_MD5));
+        executeTest("test FastaReference with contiguous intervals, different contigs", spec);
+    }
+
+    @Test
+    public void testAlternateReferenceContiguousSameContig() {
+        // Show that FastaAlternateReferenceMaker behaves the same as FastaReferenceMaker across contiguous intervals on the same contig.
+        // Note that there are variant locations in this interval.
+        WalkerTestSpec spec = new WalkerTestSpec(
+                "-T FastaAlternateReferenceMaker -R " + b36KGReference + " -V " + validationDataLocation + "NA12878.chr1_10mb_11mb.slx.indels.vcf4 -L 1:10,000,100-10,000,200 -L 1:10,000,201-10,000,301 -o %s",
+                1,
+                Arrays.asList(CONTIGUOUS_INTERVAL_SAME_CONTIG_MD5));
+        executeTest("test Alternate FastaReference with contiguous intervals, same contig", spec);
+    }
+
+    @Test
+    public void testAlternateReferenceContiguousDiffContigs() {
+        // Show that FastaAlternateReferenceMaker behaves the same as FastaReferenceMaker across contiguous intervals on different contigs.
+        // Note that there are variant locations in this interval.
+        WalkerTestSpec spec = new WalkerTestSpec(
+                "-T FastaAlternateReferenceMaker -R " + b36KGReference + " -V " + validationDataLocation + "NA12878.chr1_10mb_11mb.slx.indels.vcf4 -L 1:10,000,100-10,000,200 -L 2:10,000,201-10,000,301 -o %s",
+                1,
+                Arrays.asList(CONTIGUOUS_INTERVAL_DIFF_CONTIG_MD5));
+        executeTest("test Alternate FastaReference with contiguous intervals, different contigs", spec);
+    }
+
     @Test
     public void testIndelsAndSnpMask() {
 
         WalkerTestSpec spec = new WalkerTestSpec(
                 "-T FastaAlternateReferenceMaker -R " + b36KGReference + " -V " + validationDataLocation + "NA12878.chr1_10mb_11mb.slx.indels.vcf4 --snpmask:vcf " + b36dbSNP129 + " -L 1:10,075,000-10,075,380 -L 1:10,093,447-10,093,847 -L 1:10,271,252-10,271,452 -o %s",
                  1,
-                 Arrays.asList("ef481be9962e21d09847b8a1d4a4ff65"));
+                 Arrays.asList("375efb2feb017f01339f680fdffac6cd"));
         executeTest("test indels", spec);
     }
 
@@ -85,7 +130,7 @@ public class FastaAlternateReferenceIntegrationTest extends WalkerTest {
         WalkerTestSpec spec = new WalkerTestSpec(
                 "-T FastaAlternateReferenceMaker -R " + b36KGReference + " -V " + GATKDataLocation + "dbsnp_129_b36.vcf -L 1:10,023,400-10,023,500 -L 1:10,029,200-10,029,500 -o %s",
                  1,
-                 Arrays.asList("8b6cd2e20c381f9819aab2d270f5e641"));
+                 Arrays.asList("81e30f0ab92684c496343c8ea51a393e"));
         executeTest("test SNPs", spec);
     }
 
@@ -108,7 +153,7 @@ public class FastaAlternateReferenceIntegrationTest extends WalkerTest {
         WalkerTestSpec spec = new WalkerTestSpec(
                 "-T FastaAlternateReferenceMaker -R " + b37KGReference + " --use_IUPAC_sample NA12878 -V " + privateTestDir + "NA12878.WGS.b37.chr20.firstMB.vcf -L 20:61050-66380 -o %s",
                 1,
-                Arrays.asList("5feb2a576ff2ed1745a007eaa36448b3"));
+                Arrays.asList("8fd887bca9f3949f2c23c3565f7dcc1b"));
         executeTest("test iupac", spec);
     }
 }
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/fasta/FastaReferenceMaker.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/fasta/FastaReferenceMaker.java
index 08ab3019a..9df4579e2 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/fasta/FastaReferenceMaker.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/fasta/FastaReferenceMaker.java
@@ -55,7 +55,15 @@ import java.io.PrintStream;
  *
  * <h3>Output</h3>
  * <p>
- * A fasta file representing the requested intervals.
+ * A fasta file representing the requested intervals. Each interval has a description line starting with a greater-than (">") symbol followed by sequence data.
+ * The description begins with the contig name followed by the beginning position on the contig.
+ * <pre>
+ * For example, the fasta file for contig 1 and intervals 1:3-1:4 and 1:6-1:9
+ * >1 1:3
+ * AT
+ * >1 1:6
+ * GGGG
+ * </pre>
  * </p>
  *
  * <h3>Usage example</h3>
@@ -104,18 +112,20 @@ public class FastaReferenceMaker extends RefWalker<Pair<GenomeLoc, String>, Geno
         // if there is no interval to the left, then this is the first one
         if ( sum == null ) {
             sum = value.first;
+            fasta.setName(fasta.getName() + " " + sum.toString());
             fasta.append(value.second);
         }
-        // if the intervals don't overlap, print out the leftmost one and start a new one
+        // if the intervals are not contiguous, print out the leftmost one and start a new one
         // (end of contig or new interval)
-        else if ( value.first.getStart() != sum.getStop() + 1 ) {
+        else if ( value.first.getStart() != sum.getStop() + 1 || ! value.first.getContig().equals(sum.getContig()) ) {
             fasta.flush();
             sum = value.first;
+            fasta.setName(fasta.getName() + " " + sum.toString());
             fasta.append(value.second);
         }
         // otherwise, merge them
         else {
-            sum = getToolkit().getGenomeLocParser().setStop(sum, value.first.getStop());
+            sum = sum.setStop(sum, value.first.getStop());
             fasta.append(value.second);
         }
 		return sum;